User: Farah

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Farah70
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Posts by Farah

<prev • 93 results • page 1 of 10 • next >
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What is the most efficient way of discovering bait-prey interaction networks and mapping biological process relationships within a network?
... Hello, I was wondering if you could advise me in my following questions: From a bait-prey pull-down experiment, I have an initial interaction network of 400 proteins from String database. Then, initially, to retrieve my bait protein and its highly associated proteins from this network, I selected ...
proteomics interaction networks cytoscape cluego written 5 weeks ago by Farah70 • updated 4 weeks ago by scooter410
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Which tool for clustering (sub-networking) of protein-protein interaction networks based on the Gene Ontology Biological Process of proteins?
... Hello, I have a network of 100 proteins (without any quantitative or expression data) which I want to do clustering based on their Gene Ontology biological process inside the network to create some subnetworks of my initial network. In such a way that nodes to be coloured based on their cluster, an ...
gene ontology cytoscape clustering sub-network written 6 weeks ago by Farah70 • updated 5 weeks ago by scooter410
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Comment: C: How to detect novel proteins and non-annotated proteins from a list of MS protei
... Ok. Thank you very much. ...
written 12 months ago by Farah70
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How to detect novel proteins and non-annotated proteins from a list of MS proteins?
... Hello, I have a list of 2000 proteins from an MS experiment. All of these proteins have accession IDs (Uniprot IDs). I would like to know, from this list of proteins, how I can identify novel proteins and those proteins which are not annotated so far (in any protein databases). I would highly appr ...
proteomics mass spectrometry novel proteins written 12 months ago by Farah70
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How to modify bin interval and bars colour in a bar polar chart created by plotly package in R?
... Hello, I am trying to make a bar polar chart for spindle orientation in a quarter circle shape. My data has two columns, "Angle" and "Percentage". I used plotly package in R and the below codes to make it: library("plotly") p <- plot_ly( type = 'barpolar', r = c(54.7, 32.6, ...
bar_polar_chart R plotly radial_histogram written 12 months ago by Farah70
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Comment: C: How to modify the nodes features in Gradient1 style in Cytoscape?
... Thank you very much dear xanderpico, and so sorry for my late response as I did not receive any emails or notifications regarding the answer to my question. Many thanks for your guide and help. Best wishes, ...
written 13 months ago by Farah70
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How to make a quarter circle polar plot using ggplot2?
... Hello, I am trying to make a polar plot/chart that goes 90 degrees (from 0 to 90 degree) instead of 360 using ggplot2. I need to visualise my data (angle and frequency) similar to these quarter circle polar plots ![Figure1][1] I ran the below codes, however, It is still a 360 degree circle polar p ...
R ggplot2 coord_polar quarter-circle-polar-plot written 13 months ago by Farah70
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Comment: C: How to interpret a Stringdb interaction network of a mouse-proteomics dataset wh
... That is great. Thanks a lot for your guide. ...
written 14 months ago by Farah70
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How to interpret a Stringdb interaction network of a mouse-proteomics dataset when it is detected only in Homo sapiens organism?
... Hello, From an Immunoprecipitation/MS (pull down) analysis from mouse cells, I have a list of Accession IDs (such as P10809, P63261, Q09666, ...). I need to discover protein-protein interactions among all of these identified proteins and also specifically interactions with my bait protein (protein ...
proteomics network string interaction stringdb written 14 months ago by Farah70 • updated 14 months ago by andrew.j.skelton736.1k
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How to modify the nodes features in Gradient1 style in Cytoscape?
... Hello, After importing the proteins interactions output of String database, which is an TSV file, into Cytoscape, I used Gradient1 Node Style for my network, because I needed to have nodes in 3D style similar to Stringdb style (with both black shadow and white specular highlight over nodes). But, I ...
3d gradient1 string cytoscape written 14 months ago by Farah70 • updated 13 months ago by xanderpico330

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Popular Question 28 days ago, created a question with more than 1,000 views. For Need Help In Rcircos Package In R Software.
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